Adaptive evolution of SCML1in primates, a gene involved in male reproduction

Table 1 Neutrality tests of SCML1 in primates using maximum likelihood estimates (site-model)

Model	lnL	Estimates of parameters	2ΔlnL	Positively selected sites
M0:	-2619.84	ω = 1.169		None
M1a	-2613.21	p0 = 0.278 p1 = 0.722	13.26(1)**	Not allowed
M2a	-2599.55	p0 = 0.217 p1 = 0.660 p2 = 0.123 ω2 = 5.25	26.52(2)**	23N 153L 201T (95 =< P < 99%) 92H 242G (P > 99%)
M7	-2616.5	p = 1.096 q = 0.005 p0 = 0.892 p = 0.020		Not allowed
M8	-2599.65	q = 0.005(p1 = 0.108) ω = 5.78	33.9(3)**	3N 95S 153L 201T 270L (P > 95%) 92H 242G (P > 99%)
M8a	-2613.21	p0 = 0.278 p = 0.005 q = 1.728 (p1 = 0.722) ω = 1.0	27.3(4)**	Not allowed

Note: * refers to P < 0.05. ** refers to P < 0.01; (1): M1a versus M0, (2): M2a versus M1a, (3): M8 versus M7 (4): M8 versus M8a. The proportions of sites under positive selection and selective constraint are p1 and p0 respectively. The parameters p and q are used for the beta distribution B(p, q).

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